Three Main Goals of this File
Produce Cleaner looking code.
Identify the amount of clusters there are
Identify the top genes
expressed in each of the clusters
Save things as RDS file so I dont have to rerun the whole code
##
## The downloaded binary packages are in
## /var/folders/7n/x74qctp91rng390gx0z9hmd80000gn/T//RtmpLgjdGC/downloaded_packages
options(future.globals.maxSize = 74 * 1024^3) # 55 GB
getOption("future.globals.maxSize") #59055800320## [1] 79456894976
SO4@meta.data$sample <- factor(
SO4@meta.data$sample,
levels = c("SO1","SO4","SO2","SO3"))
DimPlot(SO4,split.by ="sample",group.by = "sample")markers.to.plot1 <- c(
"Atf3", #
"Egr1", #
"Fos", #
"Jun", #
"Junb", #
"Pappa2", #
"Cxcl10", #
"Cldn19", #
"Krt7", #
"Egf", #
"Ptger3",
"Ckb",
"Mcub",
"Fabp3",
"Foxq1",
"Vash2",
"Pamr1",
"Vegfa"
)
DotPlot(SO4,
features = markers.to.plot1,
dot.scale = 8,
dot.min = 0,
scale = FALSE,
scale.max = 100,
scale.min = 0,
col.min = -2.5,
col.max = 2.5)+
coord_flip()
## Finding Markers for each MD Sub-SUb type
## Calculating cluster type_1
## Warning: The `slot` argument of `GetAssayData()` is deprecated as of SeuratObject 5.0.0.
## ℹ Please use the `layer` argument instead.
## ℹ The deprecated feature was likely used in the Seurat package.
## Please report the issue at <https://github.com/satijalab/seurat/issues>.
## This warning is displayed once every 8 hours.
## Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
## generated.
## Warning: `PackageCheck()` was deprecated in SeuratObject 5.0.0.
## ℹ Please use `rlang::check_installed()` instead.
## ℹ The deprecated feature was likely used in the Seurat package.
## Please report the issue at <https://github.com/satijalab/seurat/issues>.
## This warning is displayed once every 8 hours.
## Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
## generated.
## For a (much!) faster implementation of the Wilcoxon Rank Sum Test,
## (default method for FindMarkers) please install the presto package
## --------------------------------------------
## install.packages('devtools')
## devtools::install_github('immunogenomics/presto')
## --------------------------------------------
## After installation of presto, Seurat will automatically use the more
## efficient implementation (no further action necessary).
## This message will be shown once per session
## Calculating cluster type_2a
## Calculating cluster type_2b
## Calculating cluster type_3
## Calculating cluster type_4
SO.markers %>%
group_by(cluster) %>%
dplyr::filter(avg_log2FC > 1) %>%
slice_head(n = 10) %>%
ungroup() -> top10
# save as excel file
MD_degs <- SO.markers %>% arrange(desc(avg_log2FC))
write.xlsx(MD_degs, file = here("jk_code", "DEGs_MD_SUBSUBclass.xlsx"), rowNames = TRUE)
DoHeatmap(SO4, features = top10$gene) + NoLegend()## Warning in DoHeatmap(SO4, features = top10$gene): The following features were
## omitted as they were not found in the scale.data slot for the SCT assay: Rsad2,
## Gbp9, Ifi47
## Warning: The `slot` argument of `FetchData()` is deprecated as of SeuratObject 5.0.0.
## ℹ Please use the `layer` argument instead.
## ℹ The deprecated feature was likely used in the Seurat package.
## Please report the issue at <https://github.com/satijalab/seurat/issues>.
## This warning is displayed once every 8 hours.
## Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
## generated.